Closed mheiser-md closed 7 years ago
@jotsetung, does that ring a bell ? Yours, Steffen
what version of xcms
are you running?
thanks for the quick reply!
xcms - 1.48.0 IPO - 1.7.5
OK, the error comes from the retcor.obiwarp
. I'll have to look into this - but am pretty busy at the moment - this might take some time.
great thank you very much! I've done some tests as well but couldn't find a solution as I'm not really familiar with how obiwarp works... what I did observe was running above files with the following obiwarp parameters (the same ones IPO uses):
gapInit = 0.0
gapExtend = 2.1
profStep = 0.7
caused the error, wheres
gapInit = 0.0
gapExtend = 2.1
profStep = 1
does not.
I had a look into the issue. From IPO perspective I can tell the following:
IPO handles the issue as follows It seems that IPO works as intended. Here the parameter combination produces an error in the retcor.obiwarp method. IPO does not crash, as it skips the failed retention time correction and continues with grouping. The failed retention time correction is penalized in the optimisation process. Thus IPO continues to optimise. Due to the penalisation IPO tries to find parameters for which the retention time correction works, but of course this can't be guaranteed. You can check by the following code:
resultRG[[length(resultRG)-1]]$target_value
where resultRG
is the return value from optimizeRetGroup()
. If retcor_done
is 1.1, then the retention time correction for the best_settings
fails. If retention time correction works, retcor_done
should be 1.
About the issue itself
To me the issue seems xcms
specific. If there is an issue with IPO itself, @jotsetung please let me know.
For a while now I've come across the following error message when running optimizeRetGroup in single core mode:
I ignored for a while, up until my data processing pipeline crashed during the retcor.obiwarp step with the above message using optimized IPO parameters. Once I reran IPO in single core mode, I could see the message was being printed for every sample, which seems to be a rare case?
With the following script the error can be reproduced:
And this is the output: The retcor step seems to stop after sample MSpos-Ex1-cyp79-48h-Ag-1_1-B,1_01_9819 in every iteration.
It looks to me like a xcms bug, but I was wondering if IPO can perform any retcor optimization with this error?